[English] 日本語
Yorodumi
- PDB-3zkx: TERNARY BACE2 XAPERONE COMPLEX -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zkx
TitleTERNARY BACE2 XAPERONE COMPLEX
Components
  • BETA-SECRETASE 2
  • XA4813
  • XA4815
KeywordsHYDROLASE
Function / homology
Function and homology information


memapsin 1 / negative regulation of amyloid precursor protein biosynthetic process / melanosome membrane / melanosome organization / peptide hormone processing / membrane protein ectodomain proteolysis / amyloid-beta metabolic process / trans-Golgi network / protein processing / glucose homeostasis ...memapsin 1 / negative regulation of amyloid precursor protein biosynthetic process / melanosome membrane / melanosome organization / peptide hormone processing / membrane protein ectodomain proteolysis / amyloid-beta metabolic process / trans-Golgi network / protein processing / glucose homeostasis / aspartic-type endopeptidase activity / endosome / endoplasmic reticulum / Golgi apparatus / proteolysis / membrane / plasma membrane
Similarity search - Function
Beta-secretase BACE2 / Beta-secretase BACE / Memapsin-like / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site ...Beta-secretase BACE2 / Beta-secretase BACE / Memapsin-like / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Immunoglobulins / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
LAMA GLAMA (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsKuglstatter, A. / Banner, D.W. / Benz, J. / Bertschinger, J. / Burger, D. / Cuppuleri, S. / Debulpaep, M. / Gast, A. / Grabulovski, D. / Gsell, B. ...Kuglstatter, A. / Banner, D.W. / Benz, J. / Bertschinger, J. / Burger, D. / Cuppuleri, S. / Debulpaep, M. / Gast, A. / Grabulovski, D. / Gsell, B. / Hilpert, H. / Huber, W. / Kusznir, E. / Laeremans, T. / Matile, H. / Rufer, A. / Schlatter, D. / Steyeart, J. / Stihle, M. / Thoma, R. / Weber, M. / Ruf, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Mapping the Conformational Space Accessible to Bace2 Using Surface Mutants and Co-Crystals with Fab-Fragments, Fynomers, and Xaperones
Authors: Banner, D.W. / Gsell, B. / Benz, J. / Bertschinger, J. / Burger, D. / Brack, S. / Cuppuleri, S. / Debulpaep, M. / Gast, A. / Grabulovski, D. / Hennig, M. / Hilpert, H. / Huber, W. / ...Authors: Banner, D.W. / Gsell, B. / Benz, J. / Bertschinger, J. / Burger, D. / Brack, S. / Cuppuleri, S. / Debulpaep, M. / Gast, A. / Grabulovski, D. / Hennig, M. / Hilpert, H. / Huber, W. / Kuglstatter, A. / Kusznir, E. / Laeremans, T. / Matile, H. / Miscenic, C. / Rufer, A. / Schlatter, D. / Steyeart, J. / Stihle, M. / Thoma, R. / Weber, M. / Ruf, A.
History
DepositionJan 25, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BETA-SECRETASE 2
B: XA4813
C: XA4815
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7205
Polymers68,6073
Non-polymers1142
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-19.6 kcal/mol
Surface area25200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.367, 153.829, 247.178
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein BETA-SECRETASE 2 / ASPARTIC-LIKE PROTEASE 56 KDA / ASPARTYL PROTEASE 1 / ASP1 / ASP 1 / BETA-SITE AMYLOID PRECURSOR ...ASPARTIC-LIKE PROTEASE 56 KDA / ASPARTYL PROTEASE 1 / ASP1 / ASP 1 / BETA-SITE AMYLOID PRECURSOR PROTEIN CLEAVING ENZYME 2 / BETA-SITE APP CLEAVING ENZYME 2 / DOWN REGION ASPARTIC PROTEASE / DRAP / MEMAPSIN-1 / MEMBRANE-ASSOCIATED ASPARTIC PROTEASE 1 / THETA-SECRETASE / BACE2


Mass: 42047.355 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR, RESIDUES 75-460 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y5Z0, memapsin 1

-
Antibody , 2 types, 2 molecules BC

#2: Antibody XA4813


Mass: 13152.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LAMA GLAMA (llama) / Plasmid: PMESY4 / Production host: ESCHERICHIA COLI (E. coli)
#3: Antibody XA4815


Mass: 13406.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LAMA GLAMA (llama) / Plasmid: PMESY4 / Production host: ESCHERICHIA COLI (E. coli)

-
Non-polymers , 3 types, 313 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.39 Å3/Da / Density % sol: 71.96 % / Description: NONE
Crystal growpH: 7 / Details: 0.2M SODIUM MALONATE, 20% PEG3350, pH 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.37→34.7 Å / Num. obs: 49549 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 67.97 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.4
Reflection shellResolution: 2.37→2.5 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.2 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZKQ

3zkq


Resolution: 2.37→34.7 Å / Cor.coef. Fo:Fc: 0.9416 / Cor.coef. Fo:Fc free: 0.9389 / SU R Cruickshank DPI: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.181 / SU Rfree Blow DPI: 0.156 / SU Rfree Cruickshank DPI: 0.155
RfactorNum. reflection% reflectionSelection details
Rfree0.2085 2502 5.07 %RANDOM
Rwork0.1849 ---
obs0.1861 49387 99.59 %-
Displacement parametersBiso mean: 66.58 Å2
Baniso -1Baniso -2Baniso -3
1-9.9482 Å20 Å20 Å2
2---15.4095 Å20 Å2
3---5.4613 Å2
Refine analyzeLuzzati coordinate error obs: 0.359 Å
Refinement stepCycle: LAST / Resolution: 2.37→34.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4541 0 5 311 4857
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014651HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.166313HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1547SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes101HARMONIC2
X-RAY DIFFRACTIONt_gen_planes689HARMONIC5
X-RAY DIFFRACTIONt_it4651HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.38
X-RAY DIFFRACTIONt_other_torsion18.44
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion605SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5028SEMIHARMONIC4
LS refinement shellResolution: 2.37→2.43 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 183 5.13 %
Rwork0.2682 3382 -
all0.2684 3565 -
obs--99.59 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8988-0.44931.09250.6146-0.74242.1618-0.0378-0.1349-0.1532-0.0517-0.0324-0.1111-0.08660.16470.0701-0.01780.00960.037-0.03780.1858-0.0609-24.576-24.111434.8618
23.1443-1.1742-0.10232.24-1.41813.5588-0.08610.0406-0.09380.15380.1050.099-0.0491-0.1575-0.0189-0.17240.0154-0.01860.09750.3014-0.0474-16.5003-39.168766.7277
34.47181.0763-1.03053.9115-0.00022.9267-0.1364-0.2594-0.25590.13840.0272-0.3259-0.04780.38680.1093-0.0089-0.0011-0.022-0.1296-0.0402-0.1125-12.6534-11.5714-7.8228
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more